Some of these are inherent in many genres of manga, while others I've seen are more a yaoi thing.
1) the jealous ex who randomly enters the manga and messes things up for the main couple
2) the newcomer who is ridiculously good-looking and tries to steal the show, and one of the main characters, from the other
3) bullying, kidnapping, blackmail...
4) "It's the only way."
5)
6) the magical make-over that turns someone unnattractive into someone drop-dead gorgeous; often unrealistic
7) damsel-in-distress plotlines
8) "You must do it in order to pay off your debt to me."
9) the character is assaulted - violently and/or romantically - and makes no struggle against it despite not wanting it
10) rich characters, particularly semes, who manipulate the world with money to the point of shattering believability
And much, much more. Have any to add? I'm sure I haven't covered nearly all of them.